[ref. ID; 5694 (David J. Patterson, 1999)]

History
The discipline of evolutionary protistology is emerging from 30 yr of considerable upheaval. Much has yet to be done to create a comprehensive and coherent understanding of eukaryote evolution and to create a matching classification scheme. The transition period is distinguished by many new concepts and by progress along variously productive routes. A major, and possibly the most solid, development of this period has been the use of patterns of ultrastructural organization to dintinguish monophyletic lineages of protists (Patterson 1994). It is for this reason that the discipline of evolutionary protistology could only develop solid foundations with the advent of reliable techniques of preservation of biological materials for electron microscopical examination. This happened in the 1960s. An older view of diversity of protists developed from a light microscopical perspective has now given way to one in which the major groups of eukaryotes are regarded as those groups that share a common cytological organization (an "ultrastructural identity"; Patterson and Brugerolle 1988).
An ultrastructural identity refers to a variety of features made visible by electron microscopy. They include (but are not restricted to) the following: the shape of the cristae in the mitochondria (cristae may be tubular, long or bleb shaped, or branching; they may be discoidal, with or without a pedicel; or they may be flat plates - only very rarely does the form of cristae vary within species or group of protists); the presense or absence of hairs, scales, or other excrescences on the flagella; the component parts of the transition region where the 9 + 2 organization of the axoneme transforms into the nine-triplet structure of the basal bodies; the length and orientation of the basal bodies and their associations with other organelles; the nature of the microtubular and other rootlet structures that arise from the basal bodies and the associations between of other microtubular or other cytoskeletal arrays within the cell, especially under the cell surface; the nature, composition, origins, and appearance of any extracelluar materials; the presence and nature of microtubule organizing centers; the number, nature, and heterogeneity of nuclei, structures within the nuclear envelope, intranuclear and paraneculear inclusions; the behavior of the nuclear envelope during mitosis (Is it retained, is it completely lost, or is it perforated in regions by the intruding spindle?); the behavior of the mitotic spindle (where does it nucleate, is it located within the nucleus or external to the nucleus, or does it start in the cytoplasm and penetrate into the nucleus?); if there is a choloplast, how many bounding membranes, how may thylakoids per lamella, the presence and nature of contained (e.g., stigma) or associated (e.g., nucleomorph) organelles; the identity and nature of other endomembranous organelles in the cell; and other idiosyncrasies.
The robustness of grouping (i.e. our hypotheses about what is related to what) defined by reference to ultrastructural identities to new data (i.e., to being tested) is virtually total (Patterson 1994). Through this process, descriptive protistology establishes major terminals or building blocks that phylogeneticists must than assemble into some form of evolutionary edifice as sister groups become evident. Several years ago, the vast majority of major taxa with a single unltrastructural identity were without sister groups. Now some of these have been brouht together to form larger and also robust groupings. Examples include euglenids and kinetoplastids within the Euglenozoa; the chrysophytes sensu lato, opalines, oomycetes, diatoms, brown algae, inter alia to form the stramenopiles; and chytrids, choanoflagellates, fungi, and animals to form the opisthokonts. A further body of data has been invaluable in seeking to explore evolutionary relationships. This is the one that incorporates the data on sequences of bases in genes. This approach has corroborated the groupings developed on the basis of ultrastructure and has suggested more extensive relationships. The first useful overall molecular trees were based on genes for the small subunit ribosomal RNA.

Classificatory Philosophies in Protistology
Evolutionary edifices usually take the form of trees (dendrograms) or of classification schemes. Some protistologists (e.g., Lipscomb 1984; Patterson 1994; Simpson 1997) are convinced of the utility of creating monophyletic and holophyletic groups (i.e. organisms from a single source and all descendants therefrom). They are consequently committed to developing classification schemes that can easily be converted into evolutionary schemes (and vice versa) by sets of simple rules that have been developed within protistology (e.g., Patterson 1986) or have been reviewed more generally (Wiley 1981). The basic logic is that the hierarchical structure within a classification scheme should reflect the sister-group relationships of the lineages. The approach is that of the phylogenetic systematists and produces a logic that can be applied to all taxa, and the fidelity and consistency of the approach can be assessed (Wiley 1981). Ideally, this should lead discussion within evolutionary protistology into a mode of progression, rather than unresolvable dispute about details that arise from incompatible philosophies. To achieve the end of phylogenetic systematics, polyphyletic groups must be eliminated and paraphyletic groups must be minimized.
Among contemporary protistologists, only Cavalier-Smith (e.g., 1998) has developed a comprehensive classification using a logic that differs from the phylosophy of phylogenetic systematics. Broadly speaking, this philosophy accepts evolutionary relationships as only one several factors that will determine groupings of organisms. The ranking the composition of taxa may (or may not) be determined by additional factors such as the "importance" of the group (e.g., Cavalier-Smith 1981, 1983, 1998).
Many of the other classification schemes of recent year (e.g., Krylov et al., 1980; Levine et al. 1980; Corliss 1984, 1994; Mohn 1984; Sleigh et al. 1984; Margulis et al. 1990; Leipe and Hausmann 1993; Hulsmann and Hausmann 1994; inter alia) have no explicit philosophy. Rather, they use a variety of criteria to create subsets of eukaryotic life. These criteria may include a desire to retain some but not all elements of historical classifications because of their familiarity (e.g., Corliss 1994). These later approaches foster subjectivism within classification. This in turn leads to the defense of paraphyletic taxa and the dispersal of the rigor that eliminates polyphyletic taxa. Speculation (here intended to refer to assertions that lack an evidential basis or are inconsistent with some evidence, or to situations where the relationship between the assertion and the evidence is ambiguous) becomes an admissible criterion by which taxa may be classified. The lack of agreed ground rules impedes the emergence of explicit arguments based on logic and data. The results are taxonomic schemes that, in their structure, fail to reveal that authors' understanding of relatedness in obvious and simple ways. A dispute arising from different approaches also directed efforts away from the fairly massive task of compiling and agreeing on all relevant and appropriate data since many schemes are flawed by not including all available information or by misinterpreting some of it (e.g., Lipscpmb 1985).
The current situation, in which there are a number of different and apparently incompatible classification schemes, is confusing for observers and participants alike. This confusion can be reduced if the discussion on philosophy can be separated from the debate on the taxa that emerge as the result of the application of the philosophy. Constructive debate on taxa only takes place within the context of its relevant philosophy and not between philosophies. The general discussion that follows is divided into a discussin on options that seem to apply within protistology. The longer part of this article elaborates an earlier effort (Patterson 1994) to list all major lineages for which no sister taxon can be identified or for which there is no agreement. The list is set in the context of phylogenetic systematics. It contributes to the assembly of a scheme of classification for the major evolutionary lines of eukaryotes in which the hierarchical structure is determined by insights into ancestor/descendent relationships. This list does not refer to schemes arising from other philosophies or taxa derived from them except where those approaches have intentionally or accidentally produced monophyletic and holophyletic groups. In a sense, the resulting list may be thought of as a boundary between understanding evolutionary relationships and ignorance.

Naming of Taxa and the Exemplar Groups, Stramenopiles and Archezoa
The following discussion of how protistologists have tended to address nomenclature, ranks, and definitions refers to two particular groups - the stramenopiles (Patterson 1989) and the Archezoa (Cavalier-Smith 1983). The groups were conceived in different ways, and reference to them helps to clarify the benefits and disadvantages of different approaches. Names are labels that refer to a collection of organisms. The naming of a taxon is an exercise that follows from the identification of a group of organisms. The way in which a name is applied is often independent of the process of defining a taxon. Although it would be ideal for there to be universal agreement on how names should be determined and used, there are few or no nomenclatural codes or guidelines as to spelling, priority, or other factors that operate above the level of family to protect stability and clarity.
The quality of a name can be judged in reference to several criteria that will protect clarity and stability. First, the link between the name and the group should be unambiguous. Each label should either refer to a definition or to a particular composition of a taxon. Second, The same name should not refer to different collectives or organisms (i.e., there should be no homonyms). Third, the meanings of names should not change with time. Finally, names should have a long life. "The stramenopiles" was a concept introduced to allow reference to a collection of protists many of which had previously been referred to as "heterokont algae," "chromophytes," "chrysophytes," or "chromists" (Patterson 1989). During their long history, earlier concepts accreted and shed various subtaxa (Green et al. 1989). This was because it was evident that algal "heterokonts" (defined by having different kinds of flagella) were related to algae that were not heterokonts (such as diatoms or kelps) and to various organisms that were "fungi" (the Oomycetes) or protozoa (opalines). The traditional groupings that relied on composition or circumscription or on key characters were providing to be ambiguous and incapable of responding to the accelerating insights of evolutionary protistology except by considerable changes in meaning of the term "heterokont". The term "stramenopiles" was introduced to refer to a similar but monophyletic and holophyletic group defined by a character innovation, that is, that group of organisms having tripartite hairs or derived from such organisms. The stability of this label is dependent on the homology of the defining synapomorphic trait (in this case, the tripartite tubular hairs). Although there is some uncertainty about whether the hairs of cryptomonads or the body hairs of proteromonads are homologous with the tripartite hairs (Green et al. 1989), the concept does appear to be robust. Although the composition of the taxon has changed, the way the name was introduced makes its meaning independent of composition. The most destabilizing factor has been the translation of the term into "tranditional" taxomony (i.e., with a rank and a diagnosis) that has led to various changed spellings (e.g., the straminipiles of Ragan and Gutell [1995]) or its treatment as synonym of alternative concepts (e.g., Lipscomb et al. 1998). The Archezoa was introduced by Cavalier-Smith (1983), which, from subsequent usage, appears to have been intended to refer to the most primitive ("basal paraphyletic") eukaryotes (Cavalier-Smith 1998). The word "Archezoa" had been introduced into the literature independently and with different meanings by Haeckel (see Copeland 1956) and by Perty (1852). The existence of homonyms is unfortunate, but Haeckel's and Perty's uses are now obsolete. Any ambiguity in respect to the homonyms can be resolved by relying on the context to clarify the meaning of the word (i.e., by stating Archezoa, sensu Cavalier-Smith 1991).

Ranks and Hierarchy
The past 30 yr have seen a proliferation of phyla and kingdoms largely among the protists. In 1964, the Society of Protozoologists created a shceme of classification with a single phylum of protozoa (Honigberg et. al. 1964). More recent classification schemes that use ranks contain dozens of phyla (e.g., Corliss 1984; Cavalier-Smith 1998) within a variable number of kingdoms. These taxonomic inflation and the use of different ranks in a short space of time is disquieting. It is not unusual to encounter statements along the lines of "the morphological and chemical uniformity of (the group) is so marked that they should be ranked only as phylum" (Cavalier-Smith 1998); there is rarely and discussion, let alone agreement, as to what criteria underpin such a statement. Ranking is consequently subjective. The same group can simultaneously or sequentially have different ranks without the acquisition of new knowledge (Patterson 1986). The rank of a given taxon may be determined by an arbitrary mixture of factors such as distinctiveness, numbers of subordinate taxa, age, sister group relationships, and ego of author. The rank of a taxon may be derived by a hierarchical structure starting from genus and going up or starting from kingdom and working done. The latter seems to be the most widespread approach but is not applied in any rigid fashion. The most reasonable approach consist with phylogenetic systematics is to assgin sister taxa the same rank. On the downside, this approach would be incomplete because we do not know all relationships and it would destabilize the existing hierarchical structure and would require a change in rank with every new insight. The term "stramenopiles" was introduced as a rankless informal name (i.e., spelled "stramenopiles", not "Stramenopiles"). The group has been included within a rankless hierarchy with subtaxa (Patterson 1994). This has not impaired its use. Some authors have sought to formalize the name and apply a rank (the Kingdom Stramenopila; Beakes 1998). The Archezoa was introduced with the rank of subkingdom and currently has this rank, although it, in the interval, has been ranked as a kingdom and as a superkingdom (Cavalier-Smith 1983, 1990, 1993, 1998). The instability of the rank suggests that it does not reflect ancestor-descendent relationships, distinctiveness of the organisms in the group, or even composition of the group because the same rank is applied to "Archezoa" with differing compositions. This particular case indicates that ranks do not need to be determined by objective criteria but are (usually?) determined by a subjective assessment of equivalency with other evolutonary concepts.